CDC and others reveal the evolution of the new coronavirus: how mutations enhance infectious power

Local time, on March 2, researchers from
five collaborating organizations, including Concord Hospital in Beijing, CDC, UCLA, the University of Pittsburgh, and Hunan University, published a major study online on bioRxiv, a bioScience preprinted website, on mutations, recombinations and insertions in the evolution of the new coronavirus ("Mutations, Recombination Insertion and Evolution of the Evolution of 2019-nCoV").
study analyzed the mutations of the virus to explain why the new coronavirus's infection performance was significantly enhanced.
team further estimated that the differences between most of the new human coronavirus (2019-nCoV) and the bat RaTG13 virus protein occurred between 2005 and 2012, while the difference between the human SARS virus and the bat SARS-like coronavirus occurred between 1990 and 2002.
point mutations, they believe there is potential evidence that recombination is also a mechanism for the evolution of 2019-nCoV. Their results suggest that the 2019-nCoV S protein may have been derived from the cer fluorescent coronavirus, rather than the bat coronavirus RaTG13. During the evolution of 2019-nCoV, there may have been a recombination between the RaTG13-like coronavirus and the case-like coronavirus strain.
The paper is co-authored by Wu Guizhen of the CDC's Viral Disease Prevention and Control Institute
, Tan Wenjie, a researcher at the Cdc's Viral Disease Prevention and Control Institute, Jiang Taixuan, director of the China Medical
Biomedical Big Data Center and assistant director of the Suzhou Institute of Systems Medicine, and Cheng Genhong, a professor in the Department of Microbiology and Immunogenetics at the University of California, Los Angeles.
team collected and analyzed 120 2019-nCoV genome sequences, including 11 new genomes from Patients from China. They found that although 2019-nCoV, human and bat SARS-CoV (Severe Acute Respiratory Syndrome Coronavirus) were highly ogeneian in the overall genome structure, they evolved into two groups of viruses with different subject entry characteristics through potential recombination of the subject binding domain (RBD).
team found that there are unique four amino acid insertions (PRRA) between the S1 and S2 domains of the hedgehog protein (S protein) in 2019-nCoV, which may be an enzyme cut point for Flynn or TMPRSS2 (transmeanthylase protease 2). Previous studies have shown that coronavirus may cleavage proteases, triggering the fusion of viral-cell membranes. This flexibility in initiating and triggering fusion mechanisms greatly regulates the pathogenicity and tendency of different coronavirus.
team suggested that the potential recombination of RBD, as well as the presence of unique Flynn protease cut points, could explain the significant increase in the infectiousness of the new coronavirus.
, 2019-nCoV has infected more than 77,000 people worldwide and killed 2,400 (as of the paper), and its genome is most similar in system development to the bat SARS virus RaTG13 strain, which was first isolated in Yunnan, China, in 2013.
researchers say there has been a lot of research so far on the new coronavirus, but the mechanisms that led to the virus infection and molecular evolution remain unclear, and the study sheds light on the evolution, specificity, and possible mechanisms to enhance infection of coronavirus B, providing a comprehensive insight into the evolution and spread of 2019-nCoV.
believe that further tracking of genomic mutations using the 2019-nCoV strain isolated from patients at different locations and at different points in time will provide an idea for understanding the molecular evolution of this rapidly spreading virus.team compared infection rates in 2019-nCoV with 2019-nCoV infection rates from the recent outbreak of the β coronavirus, the SARS virus in 2002 and the MERS virus in 2012.
2019-nCoV propagates much faster than SARS and MERS. To date, more cases of 2019-nCoV have been confirmed than during the entire SARS outbreak in 2002.
Over the past 18 years, scientists have published a number of genetic sequences of coronavirus, including SARS strains isolated from different countries during the SARS outbreak in 2002 and many MERS strains isolated from Middle Eastern countries such as Saudi Arabia and the United Arab Emirates.
team collected and sequenced 11 full-length 2019-nCoV genome sequences from new patients in several Chinese cities, including Wuhan.
system development analysis showed that the 11 new 2019-nCoV strains were similar to other 2019-nCoV strains compared to human SARS, MERS and other coronavirus strains, and were more egroidal than the Bat coronavirus RaTG13 strains.
at amino acid levels, they had only a small number of random mutations at the same consistent sequence location as the corresponding amino acid sequences in humans and bats.
In order to identify new genetic mutations, the researchers used the new coronavirus strain EPI_ISL_402125 as the root to build a system tree for the available complete genome of all 120 new coronavirus in GIAID (Global Initiative to Share Avian Influenza Data) (updated until February 18, 2020).
team found that the 2019-nCoV strain could be divided into two main categories, depending on nucleotide locations 8517 and 27641.
all strains in Group 1 (G1) have thymus at 8517 and cytosine at 27641, which is the same as the corresponding nucleotides in SARS, whereas group 2 (G2) has thymosin at 8517 and thymosin at 27641.
Epidemiological data from the above two groups of viruses show that the earliest EPI_ISL_406801 strains were collected in Wuhan on January 5, 2020, while the earliest G2 strains were isolated in Wuhan on December 24, 2019.
the presence of these two groups of genes in the same city suggests that they are coci-circulated, but that their evolution was converse in the early stages of the outbreak. In each group, the researchers also observed other common mutations in multiple strains of the virus.
based on these potentially genetic mutations and the time and location of identification, the researchers built a "mutation tree" graph to track individual shared mutations and show relationships between different isolated strains.
For example, the five strains identified in Guangdong Province between 10 January and 15 January this year belong to the first group of viruses mentioned above, all of which have the same mutation at nucleotide location 28578, indicating that they may have been transmitted by the same person. A similar virus may have spread to three cases found in Japan between January 29 and January 31, with additional mutations in the 2397 nucleotide location, and a similar virus may have spread to one case found in the United States on January 22, in which the virus had an additional mutation at the 10818 nucleotide location.
team also mentioned the location of G10818T as interesting because it was shared by several separate strains in both Group 1 and Group 2, which led to the L3606F amino acid mutation in the orf1ab polyprotein.
it is not clear whether the common mutations in groups 1 and 2 at 10,818 bits have any growth advantages, but the same L3606V mutations in the same location as the case with the bat coronavirus.
from the tree map, both strains have spread to most countries and regions where 2019-nCoV cases have been reported, with few exceptions, suggesting that both groups can spread rapidly.
the
team noted during the discussion that while the two different 2019-nCoV groups evolved before or after transmission from animals to humans, both groups were first discovered in Wuhan and then spread to different regions and countries in China. strain most closely related to the new coronavirus is RaTG13, a type β coronavirus that has previously been isolated from Chinese chrysanthemum bats. The team used nucleotide sequences to conduct other systematic developmental analyses of specific viral proteins (e.g. orf1a, S proteins, substations, and nucleoclosts) and found that the RaTG13 strain was also closely related to other bat-like SARS-like coronavirus strains.
further estimated that the differences between most 2019-nCoV and RaTG13 virus proteins occurred between 2005 and 2012, while the differences between human SARS virus and bat SARS-like coronavirus occurred between 1990 and 2002.
"Our evolutionary clock analysis estimates that 2019-nCoV split from RaTG13 and human SARS-CoV about 12 and 30 years ago, respectively," the researchers concluded during the discussion. "In addition to point mutations, there is potential evidence that recombination is also the mechanism of evolution in 2019-nCoV.
comparing full-length S protein sequences, the researchers found that the sequence between 2019-nCoV and human and bat SARS viruses was 39% esovirus and 29% esovirus with MERS or other coronavirus.
notable, the team found that the 2019-nCoV and sculpted coronavirus enjoyed almost the same amino acid sequence in the RBD (amino acid 315-550 region) of the
S protein, but not the same as RaTG13.
to confirm the findings, the team compared the previously published roller coaster CoV sequence with the previously separated but unresolved roller coaster CoV sequence.
based on comparing and systematic developmental analysis, the researchers found that the common sequence of 2019-nCoV had the highest similarity with BetaCoV/C.D./P2S/2019 (EPI_ISL_410544), while other mutations and insertion deficiencies were found in the separated armor-wearing CoV strain in Guangxi.
next, the researchers used the ML method (Maximum likelihood, the largest likelihood method) to detect a system development relationship between the common S protein sequence of 2019-nCoV and 25 representative CoV strains (including Hu-CoV, SARS and MERS) and 5 new cedar CoV strains.
results suggest that the 2019-nCoV S protein may have been derived from the latha-crust virus, rather than the bat coronavirus RaTG13, of course, both of which may be on the same spectrum as bat-SARS-CoV or bat-SL-CoVZC542.
they suggest that the entire genome structure of 2019-nCoV is most esophogenous with RaTG13, but the RBD of the S protein is the most esophogenous with the cer fluorescent CoV, a difference that suggests that recombination may have occurred between raTG13-like coronavirus and latha-like coronavirus strains during the evolution of 2019-nCoV.
researchers also examined all amino acid mutations in the genome. They found that in addition to RBD, the regions in nsp (unstrucular proteins) 14 and 15 shared continuous sequences when comparing ceder-like coronavirus with 2019-nCoV (Figure 3D). to further assess the relationship between 2019-nCoV and other SARS coronavirus, the researchers analyzed the RBM (Receptor binding motif, receptor binding motif) of 2019-nCoV and different human/bat SARS viruses and observed that they could be clearly divided into two different evolutionary branches.
evolutionary branch I viruses include 2019-nCoV, pansail CoV, and 12 species of bat SARS (Bat SARS CoV I, such as RaTG13) and human SARS virus.
evolutionary branch II virus contains 49 species of bat SARS Virus (bat SARS CoV II), such as ZXC21 and ZC45, which are about 90% ionotopic to 2019-nCoV nucleotides and amino acids.
the main difference between the two evolutionary branches is that there are 5, 13-14 amino acid regions in the RBM of evolutionary branch II viruses that are shorter than evolutionary branch I viruses.
previous studies have shown that 13-14 amino acid regions of SARS virus RBM form a unique ring structure that is stabilized by a desulfur bond between two cysteine residues. Although the amino acid sequence for 2019-nCoV in this ring region is very different from that of human SARS virus, both cysteine residues are conservative.
interesting is that all known viruses that use ACE2 as an entry receptor belong to type I, while all bat SARS viruses that do not use ACE2 to enter the receptor belong to type II. As a result, the team predicted that the type I branch virus, including 2019-nCoV, could infect host cells through human ACE2 (angiosin-converting enzyme 2), while the type II branch virus could not infect host cells through ACE2.
previous studies have concluded that SARS viruses use human ACE2 as a subject to infect host cells, while MERS viruses use DEP4 as their subject. Recent indications suggest that ACE2 is also an entry-in subject for 2019-nCoV, although other host cytokines such as TMPRSS2 may also be involved.
in evolutionary branch II viruses, although their overall genome sequences are synthogenic to 2019-nCoV, there have been no reports of viruses belonging to the branch using ACE2 to enter the subject.
Therefore, this study not only highlights the key role of RBM in determining access to subject specificity, but also raises an interesting question about how the β coronavirus's commogene strains change the trend through mutations such as insertion, absence, or recombination in RBM.
notable, the team also found that 20